[gmx-users] Simulation of membrane protein
Justin A. Lemkul
jalemkul at vt.edu
Tue Oct 18 13:09:22 CEST 2011
James Starlight wrote:
> Dear Justin,
> Indeed I didnt take into account square degree so all values presented
> in the tutorial exactly true so this was exactly my mistake. :(
> After some iterations I've obtained value for S per lipid beetween
> 0.65-0.71 A^2. This is the example of the system wich I've obtained
> after solvation and futher minimization.
> http://www.sendspace.com/file/h6urhq It looks good. :) By the way I'd
> like to know about correct value for the S per protein ? Where I can
> obtain such information for my protein ? ( e.g for big proteins such
> receptors and channels )
Such information depends on whether there is experimental evidence for the
protein you're looking for.
> The error with GenBox was due to the big vdv R for the carbons. It's
> intresting that I couldnt increase this value mush as 1.2. But my
> finally system didnt consist of some water within the membrane so I
> supose that it's good.
> Now my system on the stage of the equilibtation so I have not any
> questions yet but I only wounder to know about teqnique of the force
> fied preparation for the membrane protein simulation.
> In this work I've done this step in accordance with the tutorial. On the
> last stage I've copied gromos53a6_lipid.ff directory in $GMXLIB so now
> I can use it in pdb2gmx for instance.
> But when I've tried to make gro and top files for my lipid.pdb via
> pdb2gmx I've obtained errors that Residue 'DPP' not found in residue
> topology database so I think that in addition to the operations wich
> I've already done I should also make some changes in the
> shouldn't I?
pdb2gmx is not suited for building topologies of multi-molecule, heterogeneous
systems like solvated membranes. You may be able to get a topology, but it will
be a redundant mess. Follow the protocol in the tutorial; it avoids these
issues in the most streamlined way possible. If you need a topology of a new
lipid, create an .rtp entry (if one does not exist already) and run pdb2gmx on a
single lipid molecule. You can then #include the new .itp file in your system
> Finally, I've heard that there are already pre-build force fields for
> the membrane smulation. E.g I've heard that there is some modified
> CHARMM ff wich gave good results in simulation. Do you know something
> about this?
Various CHARMM parameter sets exist. CHARMM27 is built into the Gromacs 4.5.x
series, and CHARMM36 is available from the User Contributions section of the
> Thank you for your help,
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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